It's really not
that bad.
They've added 9 of their own to 33 of Russian Cyrillic for a total of 42 when using it for Kazakh. Now they're gonna add 6 diacritics and two digraphs, that's much less already.
Compare this to even Polish that has:
1. 9 additional letters: ą, ć, ę, ł, ń, ó, ś, ź, ż.
2. Technically no x, v nor q, but everyone knows their sound so casually or artistically you can use them, just not in 100% orthographically correct Polish.
3. 7 digraphs: ch, cz, dz, dź, dż, rz, sz.
And it's not really a problem in any way and the words are distinct enough that if you skip all the Polish specific stuff it's still 100% readable, people texting or writing online or Polish comments in code (in an ASCII file) often do that.
I've seen many systems (CJK, Arabic, Hebrew, various European ones) and have somewhat an interest in this stuff and I don't think it's a big deal at all.
I also think (as a layman) that it's really not about the system anymore but about fitting it to your language (within reason, e.g. don't try to write Polish with Chinese characters), someone could say Polish butchered Latin or gave it 16 warts but it works and I'd say the phonology is way saner than English (okay, that's not an achievement but still, no one tells English off for it's use of Latin despite it's crazy pronunciations).
I also wondered about an experiment of using both Cyrillic and Latin together at once in a language that already uses one of them to denote foreign words (e.g. Polish with foreign words in Cyrillic or Russian with foreign words in Latin), just like katakana in Japanese does (among other uses). I wonder if Kazakh writing (casual or maybe even official) with loanwords from Russian (if they exist, I don't know Kazakh, maybe they have none) might do that just for Russian foreign words, to avoid transcribing them into the Latin alphabet (which would be more awkward than just using them directly as they could in their Cyrillic which was a superset of Russian Cyrillic and would either ignore their own Latin phonology and diacritics or require a new transcription style that is unlike the other ones, thus adding to confusion).
Using Cyrillic and/or Latin of course has implications about politics, history and religion, with Cyrillic being associated with Russia, Soviet Bloc, Orthodox Christianity, etc.